nstd158 - Cleal et al 2019 - dbVar Study

nstd158 (Cleal et al. 2019)

Organism:: Human
Study Type:: Collection
Submitter:: Kez Cleal
Submitter URL:: https://www.cardiff.ac.uk/people/view/122762-baird-duncan
Description:: We performed whole genome sequencing to investigate the impact of a transit through a telomere-driven crisis on the structural integrity of the genome. We find direct evidence of telomere involvement in driving large scale complex structural rearrangement patterns during a telomere crisis. The repair signatures and configuration of these rearrangements were consistent with repair by the break-induced replication pathway. See Variant Summary counts for nstd158 in dbVar Variant Summary.
Project:: PRJNA417592
Publication(s):: Cleal et al. 2019

Links

Source: NCBI

Detailed Information: Download 1621 Variant Regions, Download 1621 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	106	106	Remapped	NC_000001.11
NC_000002.12	Chr2	126	126	Remapped	NC_000002.12
NC_000003.12	Chr3	108	108	Remapped	NC_000003.12
NC_000004.12	Chr4	91	91	Remapped	NC_000004.12
NC_000005.10	Chr5	95	95	Remapped	NC_000005.10
NC_000006.12	Chr6	107	107	Remapped	NC_000006.12
NC_000007.14	Chr7	164	164	Remapped	NC_000007.14
NC_000008.11	Chr8	171	171	Remapped	NC_000008.11
NC_000009.12	Chr9	73	73	Remapped	NC_000009.12
NC_000010.11	Chr10	113	113	Remapped	NC_000010.11
NC_000011.10	Chr11	78	78	Remapped	NC_000011.10
NC_000012.12	Chr12	54	54	Remapped	NC_000012.12
NC_000013.11	Chr13	42	42	Remapped	NC_000013.11
NC_000014.9	Chr14	41	41	Remapped	NC_000014.9
NC_000015.10	Chr15	24	24	Remapped	NC_000015.10
NC_000016.10	Chr16	48	48	Remapped	NC_000016.10
NC_000017.11	Chr17	92	92	Remapped	NC_000017.11
NC_000018.10	Chr18	58	58	Remapped	NC_000018.10
NC_000019.10	Chr19	49	49	Remapped	NC_000019.10
NC_000020.11	Chr20	48	48	Remapped	NC_000020.11
NC_000021.9	Chr21	13	13	Remapped	NC_000021.9
NC_000022.11	Chr22	23	23	Remapped	NC_000022.11
NC_000023.11	ChrX	56	56	Remapped	NC_000023.11
NC_000024.10	ChrY	3	3	Remapped	NC_000024.10
NT_113889.1	Unplaced\|NT_113889.1	4	4	Remapped	NT_113889.1
NT_113901.1	Unplaced\|NT_113901.1	3	3	Remapped	NT_113901.1
NT_167209.1	Unplaced\|NT_167209.1	1	1	Remapped	NT_167209.1
NT_167211.2	Unplaced\|NT_167211.2	2	2	Remapped	NT_167211.2
NT_167213.1	Unplaced\|NT_167213.1	5	5	Remapped	NT_167213.1
NT_167214.1	Unplaced\|NT_167214.1	47	47	Remapped	NT_167214.1
NT_167218.1	Unplaced\|NT_167218.1	2	2	Remapped	NT_167218.1
NT_187361.1	Chr1\|NT_187361.1	1	1	Remapped	NT_187361.1
NT_187518.1	Chr1\|NT_187518.1	2	2	Remapped	NT_187518.1
NT_187646.1	Chr1\|NT_187646.1	2	2	Remapped	NT_187646.1
NW_011332688.1	Chr1\|NW_011332688.1	1	1	Remapped	NW_011332688.1
NT_187527.1	Chr2\|NT_187527.1	1	1	Remapped	NT_187527.1
NW_012132915.1	Chr2\|NW_012132915.1	2	2	Remapped	NW_012132915.1
NW_012132916.1	Chr3\|NW_012132916.1	1	1	Remapped	NW_012132916.1
NW_013171801.1	Chr4\|NW_013171801.1	1	1	Remapped	NW_013171801.1
NT_113948.1	Chr5\|NT_113948.1	1	1	Remapped	NT_113948.1
NW_009646199.1	Chr5\|NW_009646199.1	1	1	Remapped	NW_009646199.1
NT_167248.2	Chr6\|NT_167248.2	1	1	Remapped	NT_167248.2
NT_113891.3	Chr6\|NT_113891.3	1	1	Remapped	NT_113891.3
NW_018654713.1	Chr6\|NW_018654713.1	1	1	Remapped	NW_018654713.1
NT_187562.1	Chr7\|NT_187562.1	2	2	Remapped	NT_187562.1
NW_003315922.2	Chr7\|NW_003315922.2	1	1	Remapped	NW_003315922.2
NW_018654714.1	Chr7\|NW_018654714.1	3	3	Remapped	NW_018654714.1
NT_187565.1	Chr8\|NT_187565.1	1	1	Remapped	NT_187565.1
NT_187567.1	Chr8\|NT_187567.1	2	2	Remapped	NT_187567.1
NT_187576.1	Chr8\|NT_187576.1	1	1	Remapped	NT_187576.1
NW_018654717.1	Chr8\|NW_018654717.1	1	1	Remapped	NW_018654717.1
NW_003315934.1	Chr10\|NW_003315934.1	1	1	Remapped	NW_003315934.1
NW_019805495.1	Chr11\|NW_019805495.1	1	1	Remapped	NW_019805495.1
NW_003315940.1	Chr12\|NW_003315940.1	1	1	Remapped	NW_003315940.1
NW_003315941.1	Chr12\|NW_003315941.1	1	1	Remapped	NW_003315941.1
NW_011332696.1	Chr12\|NW_011332696.1	1	1	Remapped	NW_011332696.1
NW_018654718.1	Chr12\|NW_018654718.1	1	1	Remapped	NW_018654718.1
NW_011332699.1	Chr13\|NW_011332699.1	2	2	Remapped	NW_011332699.1
NT_167219.1	Chr14\|NT_167219.1	16	16	Remapped	NT_167219.1
NT_187600.1	Chr14\|NT_187600.1	3	3	Remapped	NT_187600.1
NW_018654722.1	Chr14\|NW_018654722.1	2	2	Remapped	NW_018654722.1
NT_187603.1	Chr15\|NT_187603.1	1	1	Remapped	NT_187603.1
NW_003315944.2	Chr15\|NW_003315944.2	1	1	Remapped	NW_003315944.2
NW_019805500.1	Chr16\|NW_019805500.1	1	1	Remapped	NW_019805500.1
NT_113930.2	Chr17\|NT_113930.2	8	8	Remapped	NT_113930.2
NT_187614.1	Chr17\|NT_187614.1	2	2	Remapped	NT_187614.1
NT_187665.1	Chr18\|NT_187665.1	1	1	Remapped	NT_187665.1
NW_003315958.1	Chr18\|NW_003315958.1	1	1	Remapped	NW_003315958.1
NT_187693.1	Chr19\|NT_187693.1	1	1	Remapped	NT_187693.1
NW_003571061.2	Chr19\|NW_003571061.2	1	1	Remapped	NW_003571061.2
NW_003571057.2	Chr19\|NW_003571057.2	1	1	Remapped	NW_003571057.2
NW_003571058.2	Chr19\|NW_003571058.2	1	1	Remapped	NW_003571058.2
NW_003571059.2	Chr19\|NW_003571059.2	1	1	Remapped	NW_003571059.2
NW_003571060.1	Chr19\|NW_003571060.1	1	1	Remapped	NW_003571060.1
NW_003571056.2	Chr19\|NW_003571056.2	1	1	Remapped	NW_003571056.2
NW_003571055.2	Chr19\|NW_003571055.2	1	1	Remapped	NW_003571055.2
NW_003315962.1	Chr19\|NW_003315962.1	3	3	Remapped	NW_003315962.1
NW_003571054.1	Chr19\|NW_003571054.1	1	1	Remapped	NW_003571054.1
NT_187632.1	Chr22\|NT_187632.1	1	1	Remapped	NT_187632.1
NT_187635.1	ChrX\|NT_187635.1	1	1	Remapped	NT_187635.1
NW_009646209.1	ChrY\|NW_009646209.1	3	3	Remapped	NW_009646209.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	107	107	Submitted	NC_000001.10
NC_000002.11	Chr2	126	126	Submitted	NC_000002.11
NC_000003.11	Chr3	108	108	Submitted	NC_000003.11
NC_000004.11	Chr4	91	91	Submitted	NC_000004.11
NC_000005.9	Chr5	95	95	Submitted	NC_000005.9
NC_000006.11	Chr6	107	107	Submitted	NC_000006.11
NC_000007.13	Chr7	164	164	Submitted	NC_000007.13
NC_000008.10	Chr8	171	171	Submitted	NC_000008.10
NC_000009.11	Chr9	73	73	Submitted	NC_000009.11
NC_000010.10	Chr10	113	113	Submitted	NC_000010.10
NC_000011.9	Chr11	78	78	Submitted	NC_000011.9
NC_000012.11	Chr12	54	54	Submitted	NC_000012.11
NC_000013.10	Chr13	40	40	Submitted	NC_000013.10
NC_000014.8	Chr14	41	41	Submitted	NC_000014.8
NC_000015.9	Chr15	24	24	Submitted	NC_000015.9
NC_000016.9	Chr16	48	48	Submitted	NC_000016.9
NC_000017.10	Chr17	93	93	Submitted	NC_000017.10
NC_000018.9	Chr18	58	58	Submitted	NC_000018.9
NC_000019.9	Chr19	49	49	Submitted	NC_000019.9
NC_000020.10	Chr20	48	48	Submitted	NC_000020.10
NC_000021.8	Chr21	13	13	Submitted	NC_000021.8
NC_000022.10	Chr22	20	20	Submitted	NC_000022.10
NC_000023.10	ChrX	56	56	Submitted	NC_000023.10
NC_000024.9	ChrY	3	3	Submitted	NC_000024.9
NT_113889.1	Unplaced\|NT_113889.1	4	4	Submitted	NT_113889.1
NT_167211.1	Unplaced\|NT_167211.1	2	2	Submitted	NT_167211.1
NT_167212.1	Unplaced\|NT_167212.1	1	1	Submitted	NT_167212.1
NT_167213.1	Unplaced\|NT_167213.1	5	5	Submitted	NT_167213.1
NT_167214.1	Unplaced\|NT_167214.1	47	47	Submitted	NT_167214.1
NT_167218.1	Unplaced\|NT_167218.1	2	2	Submitted	NT_167218.1
NT_167219.1	Unplaced\|NT_167219.1	16	16	Submitted	NT_167219.1
NT_167229.1	Unplaced\|NT_167229.1	1	1	Submitted	NT_167229.1
NT_167235.1	Unplaced\|NT_167235.1	1	1	Submitted	NT_167235.1
NT_113923.1	Unplaced\|NT_113923.1	2	2	Submitted	NT_113923.1
NT_167209.1	Unplaced\|NT_167209.1	1	1	Submitted	NT_167209.1
NT_113891.2	Chr6\|NT_113891.2	1	1	Submitted	NT_113891.2
NT_167248.1	Chr6\|NT_167248.1	1	1	Submitted	NT_167248.1
NT_113901.1	Chr7\|NT_113901.1	3	3	Submitted	NT_113901.1
NT_113930.1	Chr17\|NT_113930.1	8	8	Submitted	NT_113930.1
NT_113948.1	Chr19\|NT_113948.1	1	1	Submitted	NT_113948.1

Remapping summary:

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000001.10	Chr1	107	85	2	0	0	37	107	85	2	0	0	37
NC_000002.11	Chr2	126	76	23	0	0	51	126	76	23	0	0	51
NC_000003.11	Chr3	108	85	4	0	0	37	108	85	4	0	0	37
NC_000004.11	Chr4	91	70	3	0	0	36	91	70	3	0	0	36
NC_000005.9	Chr5	95	63	0	0	0	63	95	63	0	0	0	63
NC_000006.11	Chr6	107	65	14	0	0	56	107	65	14	0	0	56
NC_000007.13	Chr7	164	92	27	2	0	82	164	92	27	2	0	82
NC_000008.10	Chr8	171	103	11	0	0	109	171	103	11	0	0	109
NC_000009.11	Chr9	73	51	6	0	0	32	73	51	6	0	0	32
NC_000010.10	Chr10	113	75	11	0	0	53	113	75	11	0	0	53
NC_000011.9	Chr11	78	51	3	0	0	48	78	51	3	0	0	48
NC_000012.11	Chr12	54	32	6	0	0	31	54	32	6	0	0	31
NC_000013.10	Chr13	40	33	2	0	0	10	40	33	2	0	0	10
NC_000014.8	Chr14	41	26	1	0	0	26	41	26	1	0	0	26
NC_000015.9	Chr15	24	13	2	0	0	17	24	13	2	0	0	17
NC_000016.9	Chr16	48	31	1	0	0	31	48	31	1	0	0	31
NC_000017.10	Chr17	93	48	2	0	0	85	93	48	2	0	0	85
NC_000018.9	Chr18	58	37	4	0	0	33	58	37	4	0	0	33
NC_000019.9	Chr19	49	29	5	0	0	26	49	29	5	0	0	26
NC_000020.10	Chr20	48	30	3	0	0	30	48	30	3	0	0	30
NC_000021.8	Chr21	13	5	3	0	0	10	13	5	3	0	0	10
NC_000022.10	Chr22	20	12	0	0	0	16	20	12	0	0	0	16
NC_000023.10	ChrX	56	39	6	0	0	21	56	39	6	0	0	21
NC_000024.9	ChrY	3	0	0	0	0	4	3	0	0	0	0	4
NT_113889.1	Unplaced\|NT_113889.1	4	2	0	0	0	4	4	2	0	0	0	4
NT_113891.2	Chr6\|NT_113891.2	1	0	0	0	0	2	1	0	0	0	0	2
NT_113901.1	Chr7\|NT_113901.1	3	2	0	0	0	2	3	2	0	0	0	2
NT_113923.1	Unplaced\|NT_113923.1	2	0	0	0	0	4	2	0	0	0	0	4
NT_113930.1	Chr17\|NT_113930.1	8	7	0	0	0	2	8	7	0	0	0	2
NT_113948.1	Chr19\|NT_113948.1	1	1	0	0	0	0	1	1	0	0	0	0
NT_167209.1	Unplaced\|NT_167209.1	1	0	0	0	0	2	1	0	0	0	0	2
NT_167211.1	Unplaced\|NT_167211.1	2	2	0	0	0	0	2	2	0	0	0	0
NT_167212.1	Unplaced\|NT_167212.1	1	0	0	0	0	2	1	0	0	0	0	2
NT_167213.1	Unplaced\|NT_167213.1	5	4	0	0	0	2	5	4	0	0	0	2
NT_167214.1	Unplaced\|NT_167214.1	47	6	0	0	0	82	47	6	0	0	0	82
NT_167218.1	Unplaced\|NT_167218.1	2	2	0	0	0	0	2	2	0	0	0	0
NT_167219.1	Unplaced\|NT_167219.1	16	16	0	0	0	0	16	16	0	0	0	0
NT_167229.1	Unplaced\|NT_167229.1	1	0	0	0	0	2	1	0	0	0	0	2
NT_167235.1	Unplaced\|NT_167235.1	1	0	0	0	0	2	1	0	0	0	0	2
NT_167248.1	Chr6\|NT_167248.1	1	0	0	0	0	2	1	0	0	0	0	2

Samplesets

Number of Samplesets: 1

Name:: SUB3205485 derivatives
Description:: All samples were derived from original BioSample SUB3205485.
Size:: 66
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Subject Phenotype
DB98	HCT116	DB98	Not reported
DB85	HCT116	DB85	Not reported
DB108	HCT116	DB108	Not reported
DB99	HCT116	DB99	Not reported
DB116	HCT116	DB116	Not reported
DB95	HCT116	DB95	Not reported
DB105	HCT116	DB105	Not reported
DB49	HCT116	DB49	Not reported
DB70	HCT116	DB70	Not reported
DB53	HCT116	DB53	Not reported
DB87	HCT116	DB87	Not reported
DB50	HCT116	DB50	Not reported
DB80	HCT116	DB80	Not reported
DB48	HCT116	DB48	Not reported
DB57	HCT116	DB57	Not reported
DB106	HCT116	DB106	Not reported
DB79	HCT116	DB79	Not reported
DB68	HCT116	DB68	Not reported
DB101	HCT116	DB101	Not reported
DB46	HCT116	DB46	Not reported
DB103	HCT116	DB103	Not reported
DB45	HCT116	DB45	Not reported
DB47	HCT116	DB47	Not reported
DB56	HCT116	DB56	Not reported
DB100	HCT116	DB100	Not reported
DB86	HCT116	DB86	Not reported
DB83	HCT116	DB83	Not reported
DB78	HCT116	DB78	Not reported
DB81	HCT116	DB81	Not reported
DB104	HCT116	DB104	Not reported
DB92	HCT116	DB92	Not reported
DB73	HCT116	DB73	Not reported
DB94	HCT116	DB94	Not reported
DB38	HCT116	DB38	Not reported
DB90	HCT116	DB90	Not reported
DB55	HCT116	DB55	Not reported
DB115	HCT116	DB115	Not reported
DB54	HCT116	DB54	Not reported
DB96	HCT116	DB96	Not reported
DB107	HCT116	DB107	Not reported
DB97	HCT116	DB97	Not reported
DB114	HCT116	DB114	Not reported
DB77	HCT116	DB77	Not reported
DB88	HCT116	DB88	Not reported
DB52	HCT116	DB52	Not reported
DB39	HCT116	DB39	Not reported
DB76	HCT116	DB76	Not reported
DB69	HCT116	DB69	Not reported
DB82	HCT116	DB82	Not reported
DB111	HCT116	DB111	Not reported
DB71	HCT116	DB71	Not reported
DB37	HCT116	DB37	Not reported
DB102	HCT116	DB102	Not reported
DB67	HCT116	DB67	Not reported
DB91	HCT116	DB91	Not reported
DB75	HCT116	DB75	Not reported
DB40	HCT116	DB40	Not reported
DB93	HCT116	DB93	Not reported
DB112	HCT116	DB112	Not reported
DB109	HCT116	DB109	Not reported
DB89	HCT116	DB89	Not reported
DB51	HCT116	DB51	Not reported
DB41	HCT116	DB41	Not reported
DB84	HCT116	DB84	Not reported
DB110	HCT116	DB110	Not reported
DB113	HCT116	DB113	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	Paired-end mapping	Illumina	1,621

dbVar

Database of genomic structural variation

nstd158 (Cleal et al. 2019)

Links

Detailed Information: Download 1621 Variant Regions, Download 1621 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd158 (Cleal et al. 2019)

Links

Detailed Information: Download 1621 Variant Regions, Download 1621 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37 (hg19)

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: